ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines [v2; ref status: indexed, http://f1000r.es/5mq]
Recent achievements in next-generation sequencing (NGS) technologies lead to a high demand for reuseable software components to easily compile customized analysis workflows for big genomics data. We present ViennaNGS, an integrated collection of Perl modules focused on building efficient pipelines f...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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F1000 Research Ltd
2015-07-01
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| Series: | F1000Research |
| Subjects: | |
| Online Access: | http://f1000research.com/articles/4-50/v2 |
| _version_ | 1818610843131052032 |
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| author | Michael T. Wolfinger Jörg Fallmann Florian Eggenhofer Fabian Amman |
| author_facet | Michael T. Wolfinger Jörg Fallmann Florian Eggenhofer Fabian Amman |
| author_sort | Michael T. Wolfinger |
| collection | DOAJ |
| description | Recent achievements in next-generation sequencing (NGS) technologies lead to a high demand for reuseable software components to easily compile customized analysis workflows for big genomics data. We present ViennaNGS, an integrated collection of Perl modules focused on building efficient pipelines for NGS data processing. It comes with functionality for extracting and converting features from common NGS file formats, computation and evaluation of read mapping statistics, as well as normalization of RNA abundance. Moreover, ViennaNGS provides software components for identification and characterization of splice junctions from RNA-seq data, parsing and condensing sequence motif data, automated construction of Assembly and Track Hubs for the UCSC genome browser, as well as wrapper routines for a set of commonly used NGS command line tools. |
| first_indexed | 2024-12-16T15:20:52Z |
| format | Article |
| id | doaj.art-eed8ad0a26254a26bb5fe263cc80db09 |
| institution | Directory Open Access Journal |
| issn | 2046-1402 |
| language | English |
| last_indexed | 2024-12-16T15:20:52Z |
| publishDate | 2015-07-01 |
| publisher | F1000 Research Ltd |
| record_format | Article |
| series | F1000Research |
| spelling | doaj.art-eed8ad0a26254a26bb5fe263cc80db092022-12-21T22:26:39ZengF1000 Research LtdF1000Research2046-14022015-07-01410.12688/f1000research.6157.27298ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines [v2; ref status: indexed, http://f1000r.es/5mq]Michael T. Wolfinger0Jörg Fallmann1Florian Eggenhofer2Fabian Amman3Department of Biochemistry and Molecular Cell Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, AustriaInstitute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090, Vienna, AustriaInstitute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090, Vienna, AustriaDepartment of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, AustriaRecent achievements in next-generation sequencing (NGS) technologies lead to a high demand for reuseable software components to easily compile customized analysis workflows for big genomics data. We present ViennaNGS, an integrated collection of Perl modules focused on building efficient pipelines for NGS data processing. It comes with functionality for extracting and converting features from common NGS file formats, computation and evaluation of read mapping statistics, as well as normalization of RNA abundance. Moreover, ViennaNGS provides software components for identification and characterization of splice junctions from RNA-seq data, parsing and condensing sequence motif data, automated construction of Assembly and Track Hubs for the UCSC genome browser, as well as wrapper routines for a set of commonly used NGS command line tools.http://f1000research.com/articles/4-50/v2BioinformaticsGenomics |
| spellingShingle | Michael T. Wolfinger Jörg Fallmann Florian Eggenhofer Fabian Amman ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines [v2; ref status: indexed, http://f1000r.es/5mq] F1000Research Bioinformatics Genomics |
| title | ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines [v2; ref status: indexed, http://f1000r.es/5mq] |
| title_full | ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines [v2; ref status: indexed, http://f1000r.es/5mq] |
| title_fullStr | ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines [v2; ref status: indexed, http://f1000r.es/5mq] |
| title_full_unstemmed | ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines [v2; ref status: indexed, http://f1000r.es/5mq] |
| title_short | ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines [v2; ref status: indexed, http://f1000r.es/5mq] |
| title_sort | viennangs a toolbox for building efficient next generation sequencing analysis pipelines v2 ref status indexed http f1000r es 5mq |
| topic | Bioinformatics Genomics |
| url | http://f1000research.com/articles/4-50/v2 |
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